Abstract
Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches.
Highlights
Abbreviations BUSCO Benchmarking universal single-copy orthologs DEGs Differentially expressed genes FDR False discovery rate Gene Ontology (GO) Gene ontology SEM–EDX Scanning electron microscopy—energy dispersive X-ray analysis ICP-OES Inductively coupled plasma—optical emission spectrometry KEGG Kyoto encyclopaedia of genes and genomes NCBI-nr National Center for biotechnology information-non-redundant database Pfam Protein family database qRT-PCR Quantitative real-time polymerase chain reaction QUAST Quality assessment tool for genome assemblies transcription factors (TFs) Transcription factors
The plant possesses several mechanisms to tolerate the salinity stress such as (i) accumulation of low molecular weight, water-soluble free state compounds which help in the maintenance of osmotic adjustment and plant metabolic activities (ii) selective ion-uptake such as the exclusion of sodium and maintaining higher cytosolic K+/Na+ (iii) nullifying the effect of ROS by enzymes such as catalase, SOD and APX (iv) salinity-tolerant genes associated with sodium-hydrogen antiporter activities of vacuolar membrane, plasma membrane and, genes related to ROS scavenging e nzymes[11]
Our studies showed the enrichment of 27 pathways, 24 biological processes, three molecular functions and one cellular component in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010 (FDR ≤ 0.05), which specifies the unique and distinct expression pattern of genes and metabolic pathways regulating the salinity stress in IND99-907 and Co 97010
Summary
Abbreviations BUSCO Benchmarking universal single-copy orthologs DEGs Differentially expressed genes FDR False discovery rate GO Gene ontology SEM–EDX Scanning electron microscopy—energy dispersive X-ray analysis ICP-OES Inductively coupled plasma—optical emission spectrometry KEGG Kyoto encyclopaedia of genes and genomes NCBI-nr National Center for biotechnology information-non-redundant database Pfam Protein family database qRT-PCR Quantitative real-time polymerase chain reaction QUAST Quality assessment tool for genome assemblies TF Transcription factors. The growth, productivity, and juice quality of sugarcane are affected by abiotic stresses viz., cold, salinity, and drought. The development of saline tolerant varieties, gene pools, and genomic resources are helpful in sugarcane crop improvement through conventional and biotechnological approaches. The comparative global gene expression studies are certainly helping to dissect the various genes and metabolic pathways associated with salinity or abiotic stress tolerances in plants[13]. We performed the comparative salt transcriptome studies to identify the salinity stress-responsive genes and metabolic pathways in salt-tolerant E. arundinaceus accession IND99-907 collected from saline soils Ernakulum district, Kerala, India[29] and salt-sensitive genotype Co 9 701030,31. We have identified many differentially expressed genes, enriched metabolic pathways and GO terms associated with salt tolerance in salt-tolerant E. arundinaceus accession IND99-907. The genomic resources developed from this study are useful in sugarcane crop improvement through development of genic markers and advanced biotechnological approaches
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